Data from: Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes.

Modern syntheses of eukaryote diversity assign almost all taxa to one of three groups: Amorphea, Diaphoretickes, and Excavata (comprising Discoba and Metamonada). The most glaring exception is Malawimonadidae, small heterotrophic flagellates that resemble Excavata by morphology, but group with Amorphea in most phylogenomic analyses. However, just one malawimonad, Malawimonas jakobiformis, has been studied with both morphological and molecular-phylogenetic approaches, raising the spectre of interpretation errors and phylogenetic artefacts from low taxon sampling. We report a morphological and phylogenomic study of a new deep-branching malawimonad, Gefionella okellyi n. gen. n. sp. Electron microscopy revealed all canonical features of ‘typical excavates’, including two opposed flagellar vanes (unlike M. jakobiformis but like many metamonads) and a composite fibre. Initial phylogenomic analyses grouped malawimonads with the Amorphea-related orphan lineage Collodictyon, separate from a Metamonada+Discoba clade. However, support for this topology weakened when more sophisticated evolutionary models were used, and/or fast-evolving sites and long-branching taxa (FS/LB) were excluded. Analyses of ‘-FS/LB’ datasets instead suggested a relationship between malawimonads and metamonads. The ‘malawimonad+metamonad signal’ in morphological and molecular data argues against a Metamonada+Discoba clade (i.e. the predominant concept of Excavata). A Metamonad+Discoba clade should therefore not be assumed when inferring deep-level evolutionary history in eukaryotes.当前针对真核生物多样性的现代综合研究，几乎将所有分类单元归为三大类群之一：无壁类群（Amorphea）、双鞭总类（Diaphoretickes）以及挖器类（Excavata，包含Discoba和Metamonada）。最突出的例外是马拉维单胞虫科（Malawimonadidae），这是一类小型异养鞭毛虫，形态上类似挖器类，但在多数系统基因组学分析中与无壁类群聚类。然而，目前仅对一种马拉维单胞虫——雅各布马拉维单胞虫（Malawimonas jakobiformis）同时开展了形态学与分子系统发育研究，这引发了一个担忧：分类单元采样不足可能导致解读误差与系统发育假象。本研究对一种新发现的深分支马拉维单胞虫——奥凯利氏盖菲翁虫（Gefionella okellyi n. gen. n. sp.）开展了形态学与系统基因组学研究。电子显微镜观察显示其具备“典型挖器类”的所有典型特征，包括两根相对排列的鞭毛翼（与雅各布马拉维单胞虫不同，但与多数后单胞虫类（Metamonada）一致）以及复合纤维结构。初始系统基因组学分析将马拉维单胞虫类与无壁类群相关的孤立谱系Collodictyon聚为一支，与后单胞虫类+Discoba演化支相互分离。然而，当使用更精密的进化模型，或剔除快速进化位点与长分支类群（FS/LB）后，该拓扑结构的支持率显著下降。而针对“-FS/LB”数据集的分析则显示，马拉维单胞虫类与后单胞虫类存在演化关联。形态学与分子数据中存在的“马拉维单胞虫类+后单胞虫类”信号，驳斥了“后单胞虫类+Discoba演化支”的假说（即当前主流的挖器类概念）。因此，在推断真核生物的深层演化历史时，不应预先假定存在后单胞虫类+Discoba演化支。